Biological and chemical processes can involve a number of different molecular substances interacting to produce an overall result such as the metabolism of a substrate, transmission of a chemical signal in response to a signaling molecule, activation of an immune response to an antigen, or a catalytic process converting a substrate into a product. Such biological and chemical processes are frequently represented in the form of a biological or chemical pathway representing the sequence of events and showing how the different chemical and/or biological substances involved in the process interact.
A biological pathway shows how a series of interactions occurs between chemical and/or biological substances in a cell that can lead, for example, to a certain product or change in a cell. The effect of the biological process shown in a biological pathway can include the synthesis or assembly of new molecules (e.g., proteins), the activation or deactivation, or triggering a cellular activity such as cell movement, cell division or cell death. Biological pathways include pathways showing biochemical and chemical processes involved in metabolism, the regulation of gene expression and the transmission of biological signals.
One kind of biological pathway is a metabolic pathway. A metabolic pathway shows a series of chemical reactions occurring within a cell. In a metabolic pathway, a chemical is modified by a series of chemical reactions, typically catalyzed by enzymes, and potentially involving other substances such as minerals, vitamins, and other cofactors. Since many chemicals can be involved, metabolic pathways can be quite elaborate. In addition, numerous distinct pathways can co-exist within a cell. A metabolic pathway can include a series of biochemical reactions that are connected by their intermediate where the products of one reaction are substrates for subsequent reactions. Some of the reactions in a metabolic pathway may be reversible. In addition, some of the reactions of a metabolic pathway may be subject to regulation by products formed later in the pathway, e.g., through feedback inhibition. An example of a metabolic pathway, the pathway for the metabolism of glucose to pyruvate (glycolysis), is shown in FIG. 1.
Signal transduction pathways, also called cell signaling pathways, move a signal from a cell's exterior to its interior. Different cells are able to receive specific signals through structures on their surface, called receptors. After interacting with a receptor, the signal travels through the cell where its message is transmitted by specialized proteins that trigger a specific action in the cell. For example, a chemical signal from outside the cell might be turned into a protein signal inside the cell. In turn, that protein signal may be converted into a signal that prompts the cell to move.
Another kind of biological pathway is an immunological pathway. An immunological pathway is the sequence of steps and events that are triggered when the body responds to a foreign particle (or not foreign in the case of autoimmune disorders). An immunological pathway can include metabolic pathways and can also involve partial or whole cells or viruses in addition to smaller molecular components such as enzymes and peptides. An example of an immunological pathway, the pathway involved in cell signaling in response to tumor necrosis factor alpha (TNFα), is shown in FIG. 2.
Gene regulation pathways turn genes on and off. A gene regulation pathway is a pathway by which genes are turned on or off in response to a set of conditions such as the presence or absence of a compound.
The definitions of the different kinds of biological pathways are not exclusive and different pathways may interact. Metabolic substrates or metabolites involved in metabolic pathways may initiate or become involved in cell signaling pathways or gene regulation pathways. Signal transduction pathways can be involved in the immune response so that signal transduction pathways involved in raising an immunological response can also be considered to be immunological pathways. In addition, cell signaling pathways can also lead to activation or inactivation of gene regulation pathways such that gene regulation occurs as a result of the cell signaling process.
One kind of chemical pathway is a catalytic cycle, which shows the reaction steps involved in a chemical process involving a catalyst. Often such cycles show the conversion of a pre-catalyst to a catalyst. Since catalysts are regenerated, catalytic cycles can be written as a sequence of chemical reactions in the form of a loop. In such loops, the initial step entails binding of one or more reactants by the catalyst, and the final step is the release of the product and regeneration of the catalyst. FIG. 3 shows an example of a catalytic cycle for the Wacker process, involving the palladium-catalyzed oxidation of ethylene to form acetaldehyde.
In some cases, biological and chemical pathways can show more than one possible pathway, with more than one possible route, or alternative sequence of events, that can occur through the pathway. In a metabolic pathway, for example, a given substrate can be converted to more than one possible product. FIG. 4 shows an example of such a pathway, namely the pathway for nicotine metabolism, which shows at least four possible paths for the metabolism of nicotine.
Although biological and chemical pathways represent a way of conveying information about biological and chemical processes, the figures can be complicated and difficult to interpret, and can fail to accurately convey information about molecular interactions and factors such as molecular scale, shape and spatial crowding. A scientist's understanding of a biological or chemical pathway could be improved by providing an animation or interactive scene that shows how the different steps of the biological or chemical process occur over time, and spatially represents how the biological or chemical components involved in the chemical process interact over the course of the process.